[gmx-users] Temperature coupling group and center-of-mass (COM) motion removal in simulation of protein on membrane surface

[Olga Press]

Dear all,
I would like to perform an equilibration of system in which the protein is
on DOPC bilayer surface. I have two questions regarding the .mdp file, I
would be very grateful if you can help me with them.
1. Should I couple separately the tc-grps: Protein_DOPC SOL_CLA_SOD? like
in the case of embedded proteins?
2.  Should the bilayer COM and solvent COM must be reset separately in the
following way: comm-grps = Protein_DOPC SOL_CLA_SOD?
Thanks in advance.
Olga



*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel